Differential Expression Analysis of single cell data with large difference in cell count for groups.

Question

[Saran]

Hello,

I am using Seurat to analyze scRNA data collected from 12 samples spanning 4 different tissues. I have integrated all of the samples and normalized via SCTransform.

All samples only consist of CD4+ T-Cells and I have split them into 4 groups based on expression of two genes and I see a huge difference in Cell Counts:

• CCR5+ TCF7+ : 128
• CCR5+ TCF7- : 221
• CCR5- TCF7+ : 43925
• CCR5- TCF7- : 17004

What I am wondering is if these large differences will cause any issues with differential expression analysis between the groups? It just seems odd to compare groups with such large differences and I want to know if any-one with greater expertise thinks this could be an issue.

Thank You, Sara